The storm swept through Mpumalanga's capital city between 3pm and 4pm on Sunday, uprooting trees and damaging buildings, houses and vehicles.
"A tower crane collapsed inside the stadium bowl during the storm, but luckily the head of the crane landed outside the stadium, missing the VIP section. Imagine the damage it would have caused to the VIP section if it fell inside the stadium," said host city spokesperson Ronny Moyo on Tuesday.
He said the damage to the stadium was minor and would take between one to two months to repair, without affecting the deadline for the stadium's completion.
"Our biggest challenge now is to get another crane, which will take a day to erect," he said.
He said the replacement crane would come from the Orlando Stadium in Soweto that has already been completed.
Resident engineer at the Mbombela Stadium, Leon Botha, said that besides the tower crane, damage was also done to ten precast seating beams that were either destroyed or damaged and must be replaced.
One of the 21 roof bays was extensively damaged and must be replaced, while some brick work was also damaged.
"We also experienced some minor superfluous concrete damage on the upper deck, raker beams and a concrete manhole. Some materials that were stored adjacent to the stadium were also damaged," said Botha on Tuesday.
He said the site had been closed that day, so no injuries occurred.
Botha said the stadium was more than 60% complete. Provincial culture, sports and recreation MEC, Dina Pule, has also said that the province is ahead of schedule in terms of the stadium's construction.
The stadium is scheduled to be handed over the Federation of International Football Associations (FIFA) by December, but Pule said the hand-over would take place six months earlier, in June.